Applications

Python Data 3.9-3 and RAPIDS 22.04, 5.5.2022

New versions of Python Data and RAPIDS are now available on both Puhti and Mahti. The default versions have been changed to these new versions.

CP2K 9.1 linked to Gromacs 2022, 19.4.2022

CP2K 9.1 has been linked to Gromacs 2022 for QM/MM in the module gromacs-env/2022-cp2k on Mahti. This option was previously available under the CP2K module cp2k/8.1-gmx, which has now been deprecated. Please use gromacs-env/2022-cp2k for QM/MM simulations from now on.

PyTorch 1.11, 8.4.2022

PyTorch 1.11.0 is now available in the pytorch/1.11 module on Puhti and Mahti, and has been set as the default module. See the official PyTorch 1.11 release notes, and CSC's PyTorch module documentation.

LUE released on Puhti, 5.4.2022

An approximate tool called LUE (Lustre Usage Explorer) for reporting amount of data in folders has been released on Puhti. LUE is significantly faster than standard tools like stat or du while being nicer on the file system. Please use LUE to keep track of how much data/files you have on the disk and perform clean-ups in a timely manner to ensure a more performant filesystem for all users.

Tykky 0.2.2, 31.3.2022

Tykky, a brand new tool for wrapping Conda/pip environments inside a Singularity container, has been released. Containerization will considerably improve startup times and decrease IO load with less files on the shared parallel filesystem. We recommend wrapping all existing Conda environments within containers using Tykky as the direct usage of Conda on CSC supercomputers has been deprecated.

TensorFlow 2.8, 17.3.2022

TensorFlow 2.8.0 is now available in the tensorflow/2.8 module on Puhti and Mahti, and has been set as the default module. See the TensorFlow 2.8 release notes on GitHub for more details.

Gromacs 2022, 9.3.2022

Gromacs 2022 has been installed on Puhti and Mahti and is available on both systems with module load gromacs-env/2022. A list of new features and changes is found in the Gromacs manual. gromacs-env/2021 is now the default.

CP2K 9.1, 4.3.2022

CP2K version 9.1 has been installed on Mahti and is available with module load cp2k/9.1-omp, given that gcc/10.3.0 and openmpi/4.1.0 are first loaded. A list of new features and changes is found on the CP2K website.

Schrödinger Maestro 2022.1, 25.2.2022

Schrödinger Maestro 2022.1 has been installed on Puhti and set as the default module. For a list of new features, see the Schrödinger website.

Gromacs 2021 now default version, 7.2.2022

Gromacs 2021.5 has been installed on Puhti and Mahti and set as the default module (gromacs-env).

Direct usage of Conda deprecated, 4.2.2022

CSC has deprecated the direct usage of Conda installations on our supercomputers' (Puhti and Mahti) shared file systems.

Python Data 3.9-2, 20.1.2022

A new version of Python Data is now available with module load python-data/3.9-2 on both Puhti and Mahti. It includes the most recent versions of Scikit-learn, SciPy, Pandas, JupyterLab and many other popular data analytics and machine learning packages for Python 3.9.

Python Data default module now uses Singularity, 26.11.2021

The default version of the python-data module has been changed to 3.9-1. This means that if you have been simply doing module load python-data you will now get this new version automatically. This version has been installed using Singularity which should make loading times much faster. Thanks to wrapper scripts this change should be mostly invisible to users. If you still encounter any problems, don't hesitate to report them to CSC's service desk.

Schrödinger Maestro 2021.4, 24.11.2021

Schrödinger Maestro 2021.4 has been installed on Puhti and set as the default module.

PyTorch 1.10, 10.11.2021

PyTorch 1.10.0 is now available in the pytorch/1.10 module on Puhti and Mahti, and has been set as the default module. See the official PyTorch 1.10 release notes for more details. CSC's module has the following improvements:

  • Jupyter Lab now works (previously only regular Jupyter Notebook UI worked)
  • DeepSpeed support built in (experimental support)

TensorFlow 2.7, 9.11.2021

TensorFlow 2.7.0 is now available in the tensorflow/2.7 module on Puhti and Mahti, and has been set as the default module. See the TensorFlow 2.7 release notes on GitHub for more details. CSC's module has the following improvements:

  • Jupyter Lab now works (previously only regular Jupyter Notebook UI worked)

Schrödinger Maestro 2021.3, 30.8.2021

Schrödinger Maestro 2021.3 has been installed on Puhti and set as the default module. The extended Maestro instructions have been appended with a section on how to speed up Quantum Espresso jobs. A bug in the script that generates the schrodinger.hosts file has also been fixed by setting the parallel HOST entry to use the large Slurm partition as intended.

Turbomole 7.5.1, 25.8.2021

Turbomole 7.5.1 is now available and the default module on Puhti. The most important change with this version is that the ricc2 module for performing 2nd order approximate coupled cluster calculations works appropriately, while older versions on Puhti have been recently reported to suffer from numerical instabilities. These issues do not apply to TM v7.5 installed on Mahti.

CP2K 8.2, 13.8.2021

CP2K version 8.2 has been installed on Mahti and is available with module load cp2k/8.2-omp. This requires that gcc/10.3.0 and openmpi/4.1.0 are first loaded. Version 7.1-elpa will remain the default module for now, but will be changed to 8.2-omp in the near future (despite the name, the ELPA diagonalization library is also linked to the new 8.2 version). The cp2k.psmp binary of version 8.2-omp has been tested and is roughly as efficient as 7.1-elpa.

A list of new features and changes is found on the CP2K website. Note that some keywords, such as MAP_CONSISTENT in the QS section, have been deprecated.

AMS 2021.102, 13.8.2021

AMS has been updated to version 2021.102 on both Mahti and Puhti and set as the default module. The AMS documentation has been updated accordingly to cover version 2021.102.

Molpro 2021.2, 10.8.2021

Molpro 2021.2 is now available and the default version on Puhti. List of recent changes are available on Molpro website. Our Molpro page also contains new scalability information and an example on how to use NVMe.

PyTorch 1.9, 2.7.2021

PyTorch 1.9.0 is now available in the pytorch/1.9 module on Puhti and Mahti. The module also includes the most recent versions of TorchVision, TorchAudio and TorchText. See the official release notes for more details.

Python Data 3.9, 22.6.2021

A new version of Python Data is now available with module load python-data/3.9-1 on Puhti. It includes the most recent versions of Scikit-learn, Pandas, JupyterLab and many other popular data analytics and machine learning packages for Python 3.9.

This is the first version of Python Data that has been installed using Singularity which should make loading times much faster. Thanks to wrapper scripts this change should be mostly invisible to users. If you still encounter any problems, don't hesitate to report them to CSC's service desk.

Last edited Thu May 5 2022